Diversity and distribution of anostomoid fishes (Teleostei: Characiformes) throughout the Guianas

Diversité et distribution des poissons anostomoides (Teleostei, Characiformes) dans les Guyanes. Cinquante-six espèces, soit approximativement 20% des Characiformes de la superfamille des Anostomidea (familles des Anostomidae, Chilodontidae, Curimatidae et Prochilodontidae), fréquentent les eaux douces de la Guyane française, du Guyana et du Suriname bien que ces régions ne recouvrent qu’environ 6% de la distribution naturelle de cette superfamille morphologiquement et écologiquement très diverse. Étant donnée cette grande diversité des anostomoides guyanais, les limites taxonomiques et/ou géographiques de nombreuses espèces sont mal définies, particulièrement dans la famille des Anostomidae. Ce travail combine les résultats de révisions taxonomiques antérieures à l’étude de sept collections majeures d’histoire naturelle afin de fournir des cartes de distribution et des clés d’identification de toutes les espèces d’anostomoides connues des Guyanes. Ces cartes révèlent six aires d’endémisme principales : les rivières Takutu et Ireng (bassin du Rio Branco, système de l’Amazone), Barima et Waini (bassin de l’Orénoque), le système Essequibo-Rupununi (incluant le Demerara et le Berbice), les bassins des fleuves Corantijn, Nickerie, Coppename, Saramacca et Suriname, le système Marowijne/Maroni (incluant la Litani et la Mana), et les bassins de l’Oyapock et de l’Approuague. Parmi ces six aires d’endémisme, le système Essequibo-Rupununi héberge un ensemble d’espèces exceptionnellement diversifié, résultant vraisemblablement d’échanges d’ichtyofaune entre le Rio Branco et l’Essequibo via le portail du Rupununi.Fifty-six species or approximately 20% of the Neotropical characiform superfamily Anostomoidea (families Anostomidae, Chilodontidae, Curimatidae and Prochilodontidae) occur in the freshwaters of French Guiana, Guyana, and Suriname although these regions span only approximately 6% of the native range of this morphologically and ecologically diverse superfamily. As a result of the high diversity of anostomoids in the Guianas, the taxonomic and/or geographic boundaries of many species are poorly understood, particularly within the family Anostomidae. This contribution unites results of prior taxonomic revisions with surveys of the holdings of the superfamily in seven major natural history collections to provide distribution maps and keys to the identification of all anostomoid species known to occur in the Guianas. These maps reveal six major areas of endemism: the Takutu and Ireng rivers (Rio Branco drainage, Amazon basin), the Barima and Waini rivers (Orinoco drainage), the Essequibo-Rupununi River system (including the Demerara and Berbice rivers), a union of the Corantijn, Nickerie, Coppename, Saramacca and Suriname river drainages, the Marowijne/Maroni River system (including the Litani and Mana rivers), and the Oyapock-Approuague River basins. Of these, the Essequibo- Rupununi system harbours the most exceptionally diverse assemblage of anostomoid species, likely as a result of faunal exchange between the Rio Branco and Essequibo River across the Rupununi portal.This is the publisher’s final pdf. The published article is copyrighted by Société Française d’Ichtyologie and can be found at: http://www.mnhn.fr/sfi/cybium/.Keywords: Taxonomy, Dichotomous key, Biogeography, South America, Synthesis, GeoreferencingKeywords: Taxonomy, Dichotomous key, Biogeography, South America, Synthesis, Georeferencin

Morphological diversity of the speckled dace (Rhinichthys osculus) in Oregon's desert springs

The Speckled dace (Rhinichthys osculus) is the most widespread minnow in western North America (Gilbert and Williams, 2002). It has diversified widely across its range—both morphologically and genetically—and as such might rightly be called a species complex. Our ongoing work aims to determine where boundaries between potentially undescribed species lie in Oregon and to identify morphological differences that may help diagnose those taxonomic entities. Meristic and linear morphometric data were collected from preserved specimens originating in four major drainage basins in desert Oregon. Morphometric data points to some potential phenotypic differences between fish reared in springs (slow-moving water) and fish reared in streams (fast-moving water). In particular, spring fish from each basin tend to have shallower bodies and shorter heads than the stream fish from the same basin. The morphologic differences described by this study will give insight in to the evolutionary history of this species complex and how geography has influenced the diversification of R. osculus

A new species of Sebastes (Scorpaeniformes: Sebastidae) from the northeastern Pacific, with a redescription of the blue rockfish, S. mystinus (Jordan and Gilbert, 1881)

The diverse predatory rockfishes (Sebastes spp.) support extensive commercial fisheries in the northeastern Pacific. Although 106 species of Sebastes are considered valid, many of the ecological, geographical, and morphological boundaries separating them lack clarity. We clarify one such boundary by separating the blue rockfish Sebastes mystinus (Jordan and Gilbert, 1881) into 2 species on the basis of molecular and morphological data. We redescribe S. mystinus, designate a lectotype, and describe the deacon rockfish, Sebastes diaconus n. sp. Aside from its unambiguous distinction at 6 microsatellite loci, the new species is most easily differentiated from S. mystinus by its possession of a solid in contrast with a blotched color pattern. Sebastes diaconus also possesses a prominent symphyseal knob versus a reduced or absent knob, a flat rather than rounded ventrum, and longer first and second anal-fin spines. Se bastes diaconus occurs from central California northward to British Columbia, Canada, and S. mystinus occurs from northern Oregon south to Baja California Sur, Mexico, indicating a broad region of sympatry in Oregon and northern California. Further collection and study are necessary to clarify distributional boundaries and to understand the ecology and mechanisms of segregation for this species. Additionally, fisheries assessments will need revision to account for the longstanding conflation of these 2 species.This is the publisher’s final pdf. The published article is copyrighted by United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service and can be found at: http://fisherybulletin.nmfs.noaa.gov

Enteromius pinnimaculatus (Cypriniformes: Cyprinidae), a new species from Southern Gabon

With more than 407 species of freshwater and brackish water fishes, Gabon is a country rich in ichthyological biodiversity, but its aquatic environments remain poorly explored. We present and describe a new species of Enteromius, adding to the 16 species of Enteromius currently recorded from that country. This new species is distinguished from all other Gabonese Enteromius by the presence of several distinct spots on the dorsal fin in combination with three or four round spots on the flanks. In Africa, it is superficially similar to Enteromius walkeri, and shares with that species an unusual allometry in which the proportional length of the barbels decreases as the fish grows. Nevertheless, one can distinguish these species by vertebral number, maximum standard length, the length of the anterior barbels, the length of the caudal peduncle, and in most specimens, the number of lateral-line and circumpeduncular scales. These two species also inhabit widely separated drainages, with E. walkeri occurring in coastal drainages of Ghana including the Pra and Ankobra Rivers, and the new species occurring in tributaries of the Louetsi and Bibaka rivers of Gabon, which are part of the Ogowe and Nyanga drainages, respectively. Despite extensive collections in those drainages the new species is known from only two localities, suggesting the importance of conservation of its known habitat

Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient

Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science

Fluctuations in Evolutionary Integration Allow for Big Brains and Disparate Faces

In theory, evolutionary modularity allows anatomical structures to respond differently to selective regimes, thus promoting morphological diversification. These differences can then influence the rate and direction of phenotypic evolution among structures. Here we use geometric morphometrics and phenotypic matrix statistics to compare rates of craniofacial evolution and estimate evolvability in the face and braincase modules of a clade of teleost fishes (Gymnotiformes) and a clade of mammals (Carnivora), both of which exhibit substantial craniofacial diversity. We find that the face and braincase regions of both clades display different degrees of integration. We find that the face and braincase evolve at similar rates in Gymnotiformes and the reverse in Carnivora with the braincase evolving twice as fast as the face. Estimates of evolvability and constraints in these modules suggest differential responses to selection arising from fluctuations in phylogenetic integration, thus influencing differential rates of skull-shape evolution in these two clades

A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

© 2020 by the American Society of Ichthyologists and Herpetologists. Target enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (\u3e1,000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder. In this study, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages. We perform a series of enrichment experiments using this bait set across the ostariophysan tree of life, from the deepest splits among the major groups (\u3e150 Ma) to more recent divergence events that have occurred during the last 50 million years. Our results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes

Comparative methods in R hackathon

The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative methods to understand the evolution of organismal traits and diversification. A hackathon was organized to bring together active R developers as well as end-users working on the integration of comparative phylogenetic methods within R to actively address issues of data exchange standards, code interoperability, usability, documentation quality, and the breadth of functionality for comparative methods available within R. Outcomes included a new base package for phylogenetic trees and data, a public wiki with tutorials and overviews of existing packages, code to allow Mesquite and R to interact, improvement of existing packages, and increased interaction within the community

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Abstract Background Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website ( http://www.phylotastic.org ), and a server image. Conclusions Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.http://deepblue.lib.umich.edu/bitstream/2027.42/112888/1/12859_2013_Article_5897.pd

Genetic Applications in Avian Conservation

A fundamental need in conserving species and their habitats is defining distinct entities that range from individuals to species to ecosystems and beyond (Table 1; Ryder 1986, Moritz 1994, Mayden and Wood 1995, Haig and Avise 1996, Hazevoet 1996, Palumbi and Cipriano 1998, Hebert et al. 2004, Mace 2004, Wheeler et al. 2004, Armstrong and Ball 2005, Baker 2008, Ellis et al. 2010, Winker and Haig 2010). Rapid progression in this interdisciplinary field continues at an exponential rate; thus, periodic updates on theory, techniques, and applications are important for informing practitioners and consumers of genetic information. Here, we outline conservation topics for which genetic information can be helpful, provide examples of where genetic techniques have been used best in avian conservation, and point to current technical bottlenecks that prevent better use of genomics to resolve conservation issues related to birds. We hope this review will provide geneticists and avian ecologists with a mutually beneficial dialogue on how this integrated field can solve current and future problems